suppose what I'm asking is if I'm powering my Arduino with 9V and have the USB connected acting as HID device will be OK i.e. it won't damage anything?
Perfectly OK to have both a Vin voltage and USB voltage applied at the same time, the board was designed to handle that case. The USB +5vdc never goes through the on-board +5vdc regulator because the USB power is already a regulated +5vdc voltage source coming from a PC if attached. There is a simple on-board FET switch that just turns off the USB power if the Vin voltage is of the proper value or higher.
Lefty